KpKP13 Protein target profile

Putative multidrug resistance protein mdtD

Accession: KP13_03151

Gene: AHE43633.1 mdtD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVB0
Length 471
Pocket druggability (P2Rank · AlphaFold DB model) 0.972
Direct ligand evidence 0 144 total records
Functional annotation 0 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
87.39 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.972
Structure A0A0H3GVB0
Pocket Pocket 1
Druggability (FPocket) 0.95
Structure A0A0H3GVB0
Pocket Pocket 2
ColabFold model
P2Rank 0.952 · Pocket 1
FPocket 0.863 · Pocket 35
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 88 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Chemistry

ChEMBL 4YH ChEMBL 8PR ChEMBL CEL ChEMBL CHEMBL1084589 ChEMBL CHEMBL1085319 ChEMBL CHEMBL1085320 ChEMBL CHEMBL1087296 ChEMBL CHEMBL12089 ChEMBL CHEMBL141664 ChEMBL CHEMBL142493 ChEMBL CHEMBL144721 ChEMBL CHEMBL145203 ChEMBL CHEMBL145666 ChEMBL CHEMBL148216 ChEMBL CHEMBL1502567 ChEMBL CHEMBL1630217 ChEMBL CHEMBL1630218 ChEMBL CHEMBL1642586 ChEMBL CHEMBL1651180 ChEMBL CHEMBL2048632 ChEMBL CHEMBL2158992 ChEMBL CHEMBL2158993 ChEMBL CHEMBL2158994 ChEMBL CHEMBL2158995 ChEMBL CHEMBL2158996 ChEMBL CHEMBL2158997 ChEMBL CHEMBL2158998 ChEMBL CHEMBL2158999 ChEMBL CHEMBL2159000 ChEMBL CHEMBL2159001 ChEMBL CHEMBL2159002 ChEMBL CHEMBL223643 ChEMBL CHEMBL224214 ChEMBL CHEMBL290185 ChEMBL CHEMBL328060 ChEMBL CHEMBL358518 ChEMBL CHEMBL3741903 ChEMBL CHEMBL4161736 ChEMBL CHEMBL4162139 ChEMBL CHEMBL4163342 ChEMBL CHEMBL4164426 ChEMBL CHEMBL4164617 ChEMBL CHEMBL4164737 ChEMBL CHEMBL4167074 ChEMBL CHEMBL4168026 ChEMBL CHEMBL4168315 ChEMBL CHEMBL4168943 ChEMBL CHEMBL4169246 ChEMBL CHEMBL4169284 ChEMBL CHEMBL4169953 ChEMBL CHEMBL4170063 ChEMBL CHEMBL4170066 ChEMBL CHEMBL4171005 ChEMBL CHEMBL4171147 ChEMBL CHEMBL4171241 ChEMBL CHEMBL4171337 ChEMBL CHEMBL4172225 ChEMBL CHEMBL4172372 ChEMBL CHEMBL4172500 ChEMBL CHEMBL4172781 ChEMBL CHEMBL4172832 ChEMBL CHEMBL4174957 ChEMBL CHEMBL4175014 ChEMBL CHEMBL4175717 ChEMBL CHEMBL4176162 ChEMBL CHEMBL422481 ChEMBL CHEMBL434066 ChEMBL CHEMBL4483762 ChEMBL CHEMBL4530442 ChEMBL CHEMBL463095 ChEMBL CHEMBL469266 ChEMBL CHEMBL472329 ChEMBL CHEMBL4764996 ChEMBL CHEMBL487602 ChEMBL CHEMBL5180154 ChEMBL CHEMBL5183287 ChEMBL CHEMBL5184912 ChEMBL CHEMBL5189886 ChEMBL CHEMBL5195700 ChEMBL CHEMBL5197459 ChEMBL CHEMBL519793 ChEMBL CHEMBL5199021 ChEMBL CHEMBL520369 ChEMBL CHEMBL539923 ChEMBL CHEMBL5402153 ChEMBL CHEMBL5409878 ChEMBL CHEMBL5427043 ChEMBL CHEMBL5433605 ChEMBL CHEMBL555456 ChEMBL CHEMBL772 ChEMBL CHEMBL89401 ChEMBL CHEMBL91638 ChEMBL Z80

Sequence

Primary amino-acid sequence viewer.

MTDLPASVRWQLWIVAFGFFMQSLDTTIVNTALPSMAKSLGESPLHMHMIIVSYVLTVAVMLPASGWLADRVGVRNIFFTAIVLFTAGSLFCAQASTLDQLVMARVLQGVGGAMMVPVGRLTVMKIVPRDQYMAAMTFVTLPGQVGPLLGPALGGVLVEYASWHWIFLINIPVGIVGAIATLCLMPNYTMQTRRFDLSGFLLLAAGMATLTLALDGQKGLGISPAWLAGLVAVGLCALLLYLWHARGNARALFSLNLFRNRTFSLGLGGSFAGRIGSGMLPFMTPVFLQIGLGFSPFHAGLMMIPMVLGSMGMKRIVVQVVNRFGYRRVLVASTLGLAAVSLLFMFSALAGWYYALPLVLFLQGMINASRFSSMNTLTLKDLPDDLASSGNSLLSMVMQLSMSIGVTIAGLLLGLYGQQHMSLDTASTHQVFLYTYLSMAAIIALPALIFSRVPDDVGSNTVLRRRNRSGS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

64 records
Show feature table
Start End DB Term Name
373 392 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
197 214 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
431 453 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
309 328 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
215 225 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
226 243 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
197 214 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
102 123 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
396 418 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
431 450 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
224 243 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
15 405 Pfam PF07690 Major Facilitator Superfamily
15 405 InterPro IPR011701 Major facilitator superfamily
47 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 34 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
186 196 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
76 98 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 465 Hamap MF_01577 Putative multidrug resistance protein MdtD [mdtD].
1 465 InterPro IPR023721 Multidrug resistance protein MdtD
124 134 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
135 157 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
286 308 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
97 101 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
451 471 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
102 124 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 450 SUPERFAMILY SSF103473 MFS general substrate transporter
7 450 InterPro IPR036259 MFS transporter superfamily
263 280 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
158 162 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
329 351 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
347 351 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
352 372 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
263 282 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
163 185 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
11 458 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
11 458 InterPro IPR020846 Major facilitator superfamily domain
393 416 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
396 415 PRINTS PR01036 Tetracycline resistance protein TetB signature
105 125 PRINTS PR01036 Tetracycline resistance protein TetB signature
199 217 PRINTS PR01036 Tetracycline resistance protein TetB signature
14 38 PRINTS PR01036 Tetracycline resistance protein TetB signature
135 159 PRINTS PR01036 Tetracycline resistance protein TetB signature
12 33 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
11 449 PANTHER PTHR42718 MAJOR FACILITATOR SUPERFAMILY MULTIDRUG TRANSPORTER MFSC
16 431 NCBIfam TIGR00711 DHA2 family efflux MFS transporter permease subunit
16 431 InterPro IPR004638 Drug resistance transporter EmrB-like
34 44 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
163 185 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
76 96 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
255 460 FunFam G3DSA:1.20.1250.20:FF:000021 Putative multidrug resistance protein MdtD
12 221 FunFam G3DSA:1.20.1720.10:FF:000001 Putative multidrug resistance protein MdtD
329 346 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
417 430 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
281 285 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
286 308 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
15 454 CDD cd17503 MFS_LmrB_MDR_like
65 75 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
136 158 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
45 64 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
255 457 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
255 457 InterPro IPR036259 MFS transporter superfamily
244 262 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
12 215 Gene3D G3DSA:1.20.1720.10 Multidrug resistance protein D

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.972
Likely same site as FPocket 31 5.3 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.74
Likely same site as FPocket 25 2.3 Å 11 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.147
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.124
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.107
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #2
0.95
Show in viewer
Surrounding area
Pocket 2 FPocket #25
0.488
Likely same site as P2Rank 2 2.3 Å 11 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #32
0.481 Unusual size
Show in viewer
Surrounding area
Pocket 4 FPocket #31
0.435
Likely same site as P2Rank 1 5.3 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GVB0
AlphaFold DB full sequence Viewing
ColabFold KP13_03151
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

144 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 94 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 93 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
J0M PDB via homolog 196.2 Da · LogP -3.49 · TPSA 138.5 Open detail RCSB PDB
4YH ChEMBL via homolog Detail ChEMBL
8PR ChEMBL via homolog Detail ChEMBL
CEL ChEMBL via homolog Detail ChEMBL
CHEMBL1084589 ChEMBL via homolog Detail ChEMBL

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
J0M RCSB PDB J7QAK3 196.2 Da LogP -3.49 TPSA 138.5 1 viol. ✓ Clean C([C@H]([C@@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.